In response to your issue:
I am using a 5Dmkll while theathered to a computer running EOS and using a Bowens radio trigger to fire the 2 x Bowens flash heads with one end of that communications system attached to the hot shoe with the corosponding reciever plugged into one of the flash units and also unable to use the auto focus facility simultanioulsy. This was followed by my reading the manual once again, reviewing all the online forums, checking all the connectivity between computer and camera, staring at my toes in disbelief having failed to resolve the issue.
My only work around to date is to set up the shot with the camera lens in 'auto focus' mode using the EOS 'Remote Live Shooting Window' as my guide so I can see my composition, adjust the DOF and sharp focal point, this on the computer screen using while illuminating using constant modeling lighting. Then once set up, return to the camera and change the operational mode of the physical lens from Auto back to Manual, thus locking the focus, knowing the shot is set up. Return to the computer, set the EOS control panel lighing mode to manual, then re-adjust the ISO to accomodate the flash. Shut down the 'Remote Live Shooting Window' altogether, instead open the 'Test Shooting' Window, using the assocated trigger fire the camera from that dialogue box and hey presto the flash works. Auto focus has gone out the window at this point. Once the test image materialises in the window, I set my white point against the 'in picture' grey card then take another shot to confirm all channels are equal at say 160 each and if not use the eye dropper to establish a new White Point. Confirm the adjust ment Then begin my session saving the images via the the 'Save' control within the 'Test Shot' window.
Now this is very complicated when compaired to shooting with non flash lighing which allows for full control of the camera.
However I don't imagine that this is a very proffessinal work around, and there has to be a better way, so if anyone has an alternative solution please post it as it would be most welcome.
Many thanks friends
PQA AM